Rachel Walker
Rachel Walker
@ptosco do you know if these changes fix #3965?
A few of the examples that Greg gave seem to be fixed (no clashes and RMSD between all the mols and the scaffold is < .2), including doc16404: However, doc55715,...
This is interesting! @ZontaNicola, here are the animations (sorry about the mirrored coordinates) Fragment DOF minimization stage: https://user-images.githubusercontent.com/39069546/120018608-40ecdb80-bf9c-11eb-8e7e-be5cd26ce352.mp4 FF Minimization stage: https://user-images.githubusercontent.com/39069546/120018642-5104bb00-bf9c-11eb-9210-4d5084f620df.mp4
Thank you @ptosco, and sorry for the late reply! We are going to try to update RDKit's coordinate generation method to address cases like this.
Thank you @d-b-w and @joseerlang! Closing this issue.
~This looks like the same error in the minimizer as #7671~ I looked into that issue a little bit and traced it back to some torsion energy calculations are being...
This lgtm if @greglandrum wants to take a look!
I think this looks good and is ready for @greglandrum to take a look -- these changes shouldn't impact coordinate generation at all if the `useRingTemplates` option is off. @ZontaNicola...
@ZontaNicola could what are the runtimes before and after this updated PR when running on our test set?
@phonglam3103 your smiles is not parsable, did you mean `C[C@H]1C[C@H]CC1`? If so, that code snippet is not raising issues for me `2024.09.1pre`.